Deoxyribonucleic acid (DNA) can be programmed to self-assemble reliably into diverse megadalton-scale architectures of programmed three dimensional (3D) arrangement (1 megadalton, MDa=106 daltons, 1 dalton=one twelfth of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state).
Sequence design principles for programming nucleic acids to self-assemble into highly structured, stable macromolecular assemblies date back to a landmark paper, Seeman, N C. “Nucleic acid junctions and lattices,” Journal of Theoretical Biology v99, pp237-247, 1982; and, Seeman N C, Kallenbach N R, “Design of immobile nucleic acid junctions,” Biophys J, v44 (2) pp201-209, 1983 (hereinafter Seeman). In this work, it was illustrated theoretically that canonical Watson-Crick base pairing of complementary DNA strands could in principle be used to program architectures of considerably larger-scale than the double helix itself. The core structural motifs contained in this synthetic macromolecular design paradigm were B-form DNA and the immobile four-way junction (a four-way junction that consists at high magnesium concentration of two antiparallel DNA helices in one of two possible isomeric states).
Since that work, a myriad of two dimensional (2D) and 3D structured nucleic acids have been assembled using the principles established by Seeman, exploiting a variety of topological strategies that include a highly successful approach for synthesizing large-scale DNA assemblies called scaffolded DNA origami. In the origami approach, hundreds of short synthetic single-stranded nucleic acids are combined with a single longer scaffold strand that is typically the M13 phage genome to program megadalton-scale architectures. Examples include brick-like rectilinear and curved assemblies designed on square and honeycomb lattices in which parallel DNA helices are constrained to their topologically adjoined neighbors via stacked four-way junctions, generalized gridiron-like rectilinear and curved objects in 2D and 3D, as well as other examples. In cases where a scaffold strand is not included, single-stranded helices can alternatively be assembled alone to form extended 2D and 3D lattices and crystals.
While rules for pairing nucleic acid bases and assembly conditions to design synthetic DNA architectures are now established, structure-based models that relate underlying DNA topology and base pairing to precise 3D solution structure (position and orientation of bases and base pairs, the latter abbreviated bp) and mechanical properties are lacking. A recent approach used finite element modeling based on coordinates relative to an underlying square or honeycomb (hexagonal) lattice (see D N Kim, F Kilchherr, H Dietz, M Bathe, “Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures,” Nucleic Acids Research, v40 (7) pp2862-8, 2012; and, K Pan, E Boulais, L Yang, M Bathe, “Structure-based model for light-harvesting properties of nucleic acid nanostructures,” Nucleic Acids Research, v42 (4), pp 2159-70, 2013, the entire contents of each of which are hereby incorporated by reference as if fully set forth herein). In those approaches, it was assumed that neighboring duplexes are anti-parallel and rigidly constrained to reside on one of several predetermined lattices. While useful, this lattice-based design paradigm is not generally applicable to DNA architectures containing junction motifs that do not reside on one of these lattices, significantly limiting the scope of the paradigm.